User: lkmklsmn

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lkmklsmn900
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1 year ago
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6 years, 7 months ago
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Posts by lkmklsmn

<prev • 93 results • page 1 of 10 • next >
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Order of reads in FASTQ file
... Hi biostars, FASTQ files contain sequencing reads 'as they come off the sequencing instrument' (https://genome.ucsc.edu/ENCODE/fileFormats.html#FASTQ). Is there any particular order to them? E.g. based on the position of the flow cell? Quality? Thanks in advance. ...
fastq rna-seq written 2.7 years ago by lkmklsmn900 • updated 2.7 years ago by Brian Bushnell17k
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Comment: C: ribosomal RNA contamination
... Thanks! Its true that some of the samples had low RINs. Is there any way to correct for this? And still use the samples. As of right now, PCA clustering does not reveal my treatment structure and I am worried these samples are unusable. ...
written 2.9 years ago by lkmklsmn900
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ribosomal RNA contamination
... Hi, I am working on a RNAseq data set of about 20 human tissue samples. However, some of the samples have a very low alignment rate (~30-40%) while the rest has a a decent alignment rate around 80%. I aligned the reads using STAR with default settings. The log file tells me that for those samples ...
rnaseq rrna contamination written 2.9 years ago by lkmklsmn900 • updated 2.9 years ago by Devon Ryan93k
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Total RNA RNA-seq database
... Hi, I am looking for some sort of database/compilation of RNA-seq data that allows me to quickly search by RNA-extraction protocol. More particular, I am interested in ALL GEO deposited RNA-seq datasets which extracted total RNA (as opposed to polyadenylated extraction protocols). Is there are lis ...
extraction protocol rna-seq written 2.9 years ago by lkmklsmn900 • updated 19 months ago by Biostar ♦♦ 20
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Comment: C: Ribosomal RNA in RNA-seq data
... Thanks. Yes the percentage of multi-mapping reads is very high in those affected samples. Given that only a subset of the samples are affected by this (Alignment rate<50%) my conclusion is that there must have been some error in the rRNA depletion step. ...
written 3.0 years ago by lkmklsmn900
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Ribosomal RNA in RNA-seq data
... Hi biostars, I am analyzing RNA-seq data (not for the first time) but for a subset of samples I am getting a very low alignment rate (~30%). To find out what is going on I have looked at some of the unaligned reads and they seem to come from ribosomal RNA. Now my question: Are ribosomal RNA sequ ...
rrna mapping rna-seq ribosomal written 3.0 years ago by lkmklsmn900
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Answer: A: Kallisto New RNA-seq quantification method discussion
... I find the pseudo alignment approach (kallisto, salmon, sailfish) very innovative. However, I would like to point out that RNA-seq data carries a lot more information than just gene expression levels. In my opinion the gene-level output of RNA-seq data is an alignment and not just an expression esti ...
written 3.6 years ago by lkmklsmn900
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IGV zoom into alignment
... I am using IGV to look at some RNA-seq alignment. In general I find this tool extremely helpful. However, when looking at some longer genes I am unable to visualize the alignment and I receive the message: "Zoom in to see alignment". Is there a way to change this setting to visualize the entire ge ...
rna-seq igv written 3.7 years ago by lkmklsmn900 • updated 3.7 years ago by igor8.9k
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Answer: A: How to add a new column with consecutive integer number in a bed file?
... From the command line: seq 1 n | paste bedfile - > bedfileWithInteger ...
written 3.7 years ago by lkmklsmn900
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Download ICGC gene expression data
... Can I download gene expression data from ICGC? If so, how? Do I need controlled access? ...
icgc gene expression download cancer written 3.7 years ago by lkmklsmn900 • updated 3.7 years ago by zlira80

Latest awards to lkmklsmn

Great Question 18 months ago, created a question with more than 5,000 views. For Fragment length Distribution
Epic Question 18 months ago, created a question with more than 10,000 views. For Cytoscape Or Gephi?
Popular Question 18 months ago, created a question with more than 1,000 views. For featureCounts duplicate counting
Popular Question 18 months ago, created a question with more than 1,000 views. For Convert STAR sjdb to gtf
Student 18 months ago, asked a question with at least 3 up-votes. For Convert IMPUTE2 to VCF while keeping phase information
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Any tools to quantify intron retention in RNAseq data?
Great Question 2.7 years ago, created a question with more than 5,000 views. For Fragment length Distribution
Popular Question 2.7 years ago, created a question with more than 1,000 views. For featureCounts duplicate counting
Appreciated 2.7 years ago, created a post with more than 5 votes. For Star Or Tophat?
Great Question 2.7 years ago, created a question with more than 5,000 views. For Cytoscape Or Gephi?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Convert STAR sjdb to gtf
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Fragment length Distribution
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: R programming: compare columns to column and get the mismatch
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Download ICGC gene expression data
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to convert IMPUTE2 to VCF format
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Allele Definitions Between Dbsnp And Illumina
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Convert IMPUTE2 to VCF while keeping phase information
Student 2.7 years ago, asked a question with at least 3 up-votes. For Star Or Tophat?
Epic Question 2.7 years ago, created a question with more than 10,000 views. For Star Or Tophat?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Cytoscape Or Gephi?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Cytoscape Or Gephi?
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Popular Question 3.4 years ago, created a question with more than 1,000 views. For Fast Rna-Seq Exon Count Calculation
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Cytoscape Or Gephi?
Great Question 3.6 years ago, created a question with more than 5,000 views. For Multi-Panel Heatmaps In R

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